Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $\beta$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog

Rolewicz-type chaotic operators

In this article we introduce a new class of Rolewicz-type operators in l_p, $1 \le p < \infty$. We exhibit a collection F of cardinality continuum of operators of this type which are chaotic and remain so under almost all finite linear combinations, provided that the linear combination has sufficiently large norm. As a corollary to our main result we also obtain that there exists a countable collection of such operators whose all finite linear combinations are chaotic provided that they have sufficiently large norm.Comment: 15 page

A simple Monte Carlo model for crowd dynamics

In this paper we introduce a simple Monte Carlo method for simulating the dynamics of a crowd. Within our model a collection of hard-disk agents is subjected to a series of two-stage steps, implying (i) the displacement of one specific agent followed by (ii) a rearrangement of the rest of the group through a Monte Carlo dynamics. The rules for the combined steps are determined by the specific setting of the granular flow, so that our scheme should be easily adapted to describe crowd dynamics issues of many sorts, from stampedes in panic scenarios to organized flow around obstacles or through bottlenecks. We validate our scheme by computing the serving times statistics of a group of agents crowding to be served around a desk. In the case of a size homogeneous crowd, we recover intuitive results prompted by physical sense. However, as a further illustration of our theoretical framework, we show that heterogeneous systems display a less obvious behavior, as smaller agents feature shorter serving times. Finally, we analyze our results in the light of known properties of non-equilibrium hard-disk fluids and discuss general implications of our model.Comment: to be published in Physical Review

The IR-Completion of Gravity: What happens at Hubble Scales?

We have recently proposed an "Ultra-Strong" version of the Equivalence Principle (EP) that is not satisfied by standard semiclassical gravity. In the theory that we are conjecturing, the vacuum expectation value of the (bare) energy momentum tensor is exactly the same as in flat space: quartically divergent with the cut-off and with no spacetime dependent (subleading) ter ms. The presence of such terms seems in fact related to some known difficulties, such as the black hole information loss and the cosmological constant problem. Since the terms that we want to get rid of are subleading in the high-momentum expansion, we attempt to explore the conjectured theory by "IR-completing" GR. We consider a scalar field in a flat FRW Universe and isolate the first IR-correction to its Fourier modes operators that kills the quadratic (next to leading) time dependent divergence of the stress energy tensor VEV. Analogously to other modifications of field operators that have been proposed in the literature (typically in the UV), the present approach seems to suggest a breakdown (here, in the IR, at large distances) of the metric manifold description. We show that corrections to GR are in fact very tiny, become effective at distances comparable to the inverse curvature and do not contain any adjustable parameter. Finally, we derive some cosmological implications. By studying the consistency of the canonical commutation relations, we infer a correction to the distance between two comoving observers, which grows as the scale factor only when small compared to the Hubble length, but gets relevant corrections otherwise. The corrections to cosmological distance measures are also calculable and, for a spatially flat matter dominated Universe, go in the direction of an effective positive acceleration.Comment: 27 pages, 2 figures. Final version, references adde

Multifunctions determined by integrable functions

Integral properties of multifunctions determined by vector valued functions are presented. Such multifunctions quite often serve as examples and counterexamples. In particular it can be observed that the properties of being integrable in the sense of Bochner, McShane or Birkhoff can be transferred to the generated multifunction while Henstock integrability does not guarantee i

Experimental quantum cosmology in time-dependent optical media

It is possible to construct artificial spacetime geometries for light by using intense laser pulses that modify the spatiotemporal properties of an optical medium. Here we theoretically investigate experimental possibilities for studying spacetime metrics of the form $\textrm{d}s^2=c^2\textrm{d}t^2-\eta(t)^2\textrm{d}x^2$. By tailoring the laser pulse shape and medium properties, it is possible to create a refractive index variation $n=n(t)$ that can be identified with $\eta(t)$. Starting from a perturbative solution to a generalised Hopfield model for the medium described by an $n=n(t)$ we provide estimates for the number of photons generated by the time-dependent spacetime. The simplest example is that of a uniformly varying $\eta(t)$ that therefore describes the Robertson-Walker metric, i.e. a cosmological expansion. The number of photon pairs generated in experimentally feasible conditions appears to be extremely small. However, large photon production can be obtained by periodically modulating the medium and thus resorting to a resonant enhancement similar to that observed in the dynamical Casimir effect. Curiously, the spacetime metric in this case closely resembles that of a gravitational wave. Motivated by this analogy we show that a periodic gravitational wave can indeed act as an amplifier for photons. The emission for an actual gravitational wave will be very weak but should be readily observable in the laboratory analogue.Comment: Version accepted fro publication in New Journal of Physic

Determining the carrier-envelope phase of intense few-cycle laser pulses

The electromagnetic radiation emitted by an ultra-relativistic accelerated electron is extremely sensitive to the precise shape of the field driving the electron. We show that the angular distribution of the photons emitted by an electron via multiphoton Compton scattering off an intense (I>10^{20}\;\text{W/cm^2}), few-cycle laser pulse provides a direct way of determining the carrier-envelope phase of the driving laser field. Our calculations take into account exactly the laser field, include relativistic and quantum effects and are in principle applicable to presently available and future foreseen ultra-strong laser facilities.Comment: 4 pages, 2 figure